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Revision as of 10:23, 10 December 2014
, 10:23, 10 December 2014→Running GotCloud/GenomeSTRiP Genotyping Pipeline
The discovery pipeline only performs discovery of variant sites with filtering. You will need to iterate BAMs again to perform genotyping.
The discovery pipeline only performs discovery of variant sites with filtering. You will need to iterate BAMs again to perform genotyping.
* If running on a small machine, you may want to reduce <code>--numjobs</code> from 4 to 1.
* If running on a small machine, you may want to reduce <code>--numjobs</code> from 4 to 1.
time perl ${SS}/svtoolkit/bin/genomestrip.pl -run-genotype --metadata ${SS}/svtoolkit/metadata --conf ${SS}/gotcloud.conf --numjobs 4 --region 22:36000000-37000000 --base-prefix ${SS} --outdir ${OUT} --gcroot ${GC}
time perl ${GC}/bin/genomestrip.pl --run-genotype --metadata ${SS}/metadata --conf ${SS}/gotcloud.conf --numjobs 2 --base-prefix ${SS} --outdir ${OUT}
This will take ~3 minutes to finish.
This will take ~3 minutes to finish.
